Sodium in PDB 5wqk: Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1

The structure of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1, PDB code: 5wqk was solved by Y.Suwanai, S.Toma-Fukai, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.328, 149.686, 54.013, 90.00, 110.08, 90.00
R / Rfree (%)	17.5 / 22.1

The binding sites of Sodium atom in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 (pdb code 5wqk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1, PDB code: 5wqk:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:6.6 occ:1.00 O A:SER250 2.2 6.4 1.0 O A:ASP273 2.3 5.0 1.0 O A:HIS74 2.4 5.7 1.0 OD1 A:ASP273 2.4 5.7 1.0 O A:ASP73 2.6 7.0 1.0 C A:HIS74 3.0 5.8 1.0 SD A:MET75 3.2 6.1 1.0 C A:ASP273 3.3 4.7 1.0 CG A:ASP273 3.3 5.0 1.0 C A:SER250 3.4 6.2 1.0 N A:MET75 3.6 6.0 1.0 CA A:MET75 3.7 6.0 1.0 C A:ASP73 3.8 6.8 1.0 CA A:HIS74 3.9 6.6 1.0 CA A:ASP273 3.9 4.7 1.0 CB A:HIS74 4.0 7.3 1.0 O A:HOH517 4.0 5.6 1.0 OD2 A:ASP273 4.1 5.6 1.0 NH1 A:ARG112 4.1 7.6 1.0 CB A:ASP273 4.1 4.8 1.0 N A:GLY251 4.2 5.9 1.0 CG A:MET75 4.2 5.8 1.0 CA A:GLY251 4.2 6.3 1.0 CA A:SER250 4.3 6.4 1.0 N A:HIS74 4.3 6.8 1.0 NH2 A:ARG112 4.3 8.0 1.0 N A:GLY274 4.3 4.2 1.0 CE A:MET75 4.5 6.5 1.0 CZ A:ARG112 4.6 7.6 1.0 CA A:GLY274 4.6 4.3 1.0 CB A:MET75 4.6 5.8 1.0 CB A:SER250 4.6 7.2 1.0 C A:GLY274 4.8 4.5 1.0 C A:MET75 4.8 6.0 1.0 O A:GLY274 4.9 4.4 1.0 C A:GLY251 5.0 6.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:18.8 occ:1.00 O A:HOH592 2.2 24.8 1.0 O A:HOH559 2.3 14.2 1.0 O A:ARG197 2.5 12.6 1.0 O A:GLU195 2.5 10.7 1.0 O A:HOH468 2.5 25.9 1.0 O A:ILE200 2.8 13.8 1.0 C A:ARG197 3.5 14.7 1.0 C A:GLU195 3.5 11.8 1.0 CB A:GLU195 3.9 10.0 1.0 C A:ILE200 4.0 12.5 1.0 CA A:ASP198 4.0 17.0 1.0 N A:GLU195 4.1 11.3 1.0 CA A:GLU195 4.1 10.8 1.0 N A:ASP198 4.1 14.3 1.0 N A:ILE200 4.1 13.7 1.0 N A:ARG197 4.3 14.9 1.0 N A:GLY199 4.3 18.0 1.0 C A:PRO196 4.5 14.4 1.0 C A:ASP198 4.5 17.1 1.0 CA A:ILE200 4.5 11.9 1.0 CA A:ARG197 4.5 15.2 1.0 OE1 A:GLU201 4.5 12.5 0.6 N A:PRO196 4.6 12.5 1.0 O A:PRO196 4.7 11.6 1.0 OE2 A:GLU201 4.8 13.8 0.6 CB A:ILE200 4.8 11.0 1.0 CD A:GLU201 4.9 13.1 0.6 CA A:PRO196 4.9 13.8 1.0 C A:PRO194 5.0 12.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:7.7 occ:1.00 O B:SER250 2.3 6.6 1.0 OD1 B:ASP273 2.3 7.2 1.0 O B:ASP273 2.3 7.1 1.0 O B:HIS74 2.3 7.0 1.0 O B:ASP73 2.6 6.0 1.0 C B:HIS74 3.0 7.1 1.0 SD B:MET75 3.2 6.4 1.0 C B:ASP273 3.3 6.7 1.0 CG B:ASP273 3.3 7.1 1.0 C B:SER250 3.3 7.2 1.0 N B:MET75 3.6 6.3 1.0 CA B:MET75 3.8 6.6 1.0 C B:ASP73 3.8 6.6 1.0 CA B:ASP273 3.9 6.4 1.0 CA B:HIS74 3.9 7.1 1.0 O B:HOH451 4.0 6.1 1.0 CB B:HIS74 4.0 7.8 1.0 OD2 B:ASP273 4.0 7.6 1.0 NH1 B:ARG112 4.1 10.5 1.0 CB B:ASP273 4.1 6.9 1.0 N B:GLY251 4.1 7.3 1.0 CA B:GLY251 4.1 7.5 1.0 CG B:MET75 4.2 6.1 1.0 N B:GLY274 4.3 6.1 1.0 N B:HIS74 4.3 6.6 1.0 CA B:SER250 4.3 7.5 1.0 NH2 B:ARG112 4.4 11.1 1.0 CE B:MET75 4.4 6.5 1.0 CZ B:ARG112 4.5 10.7 1.0 CA B:GLY274 4.6 5.9 1.0 CB B:MET75 4.6 6.2 1.0 CB B:SER250 4.6 8.2 1.0 C B:GLY274 4.8 6.1 1.0 C B:MET75 4.9 6.9 1.0 O B:GLY274 4.9 6.2 1.0 C B:GLY251 4.9 7.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in Complex with COMPOUND1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:23.9 occ:1.00 O B:HOH471 2.4 13.9 1.0 O B:ARG197 2.4 16.9 1.0 O B:HOH508 2.5 22.7 1.0 O B:GLU195 2.6 14.3 1.0 O B:ILE200 2.8 17.5 1.0 C B:ARG197 3.4 17.7 1.0 C B:GLU195 3.5 14.3 1.0 CB B:GLU195 3.8 12.4 1.0 C B:ILE200 3.9 15.1 1.0 N B:GLU195 3.9 13.6 1.0 CA B:ASP198 4.0 20.8 1.0 CA B:GLU195 4.0 13.2 1.0 N B:ASP198 4.1 18.8 1.0 N B:ILE200 4.1 15.7 1.0 N B:ARG197 4.3 17.0 1.0 N B:GLY199 4.3 20.2 1.0 CA B:ARG197 4.4 18.0 1.0 C B:PRO196 4.4 17.5 1.0 OE1 B:GLU201 4.5 27.4 1.0 C B:ASP198 4.5 21.1 1.0 CA B:ILE200 4.5 14.3 1.0 N B:PRO196 4.6 14.2 1.0 O B:PRO196 4.7 14.5 1.0 CB B:ILE200 4.8 12.9 1.0 OE2 B:GLU201 4.8 31.2 1.0 CD B:GLU201 4.9 27.4 1.0 C B:PRO194 4.9 13.9 1.0 CA B:PRO196 4.9 14.5 1.0 CB B:PRO194 5.0 16.3 1.0 N B:GLU201 5.0 14.2 1.0

K.Hanaoka, K.Sasakura, Y.Suwanai, S.Toma-Fukai, K.Shimamoto, Y.Takano, N.Shibuya, T.Terai, T.Komatsu, T.Ueno, Y.Ogasawara, Y.Tsuchiya, Y.Watanabe, H.Kimura, C.Wang, M.Uchiyama, H.Kojima, T.Okabe, Y.Urano, T.Shimizu, T.Nagano. Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-Producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-Site Cysteine Persulfide Sci Rep V. 7 40227 2017.
ISSN: ESSN 2045-2322
PubMed: 28079151
DOI: 10.1038/SREP40227